Abstract

The various benefits of light sheet microscopy have made it a widely used modality for capturing three-dimensional images. It is mostly used for fluorescence imaging, but recently another technique called light sheet tomography solely relying on scattering was presented. The method was successfully applied to imaging of plant roots in transparent soil, but is limited when it comes to more turbid samples. This study presents a polarised light sheet tomography system and its advantages when imaging in highly scattering turbid media. The experimental configuration is guided by Monte Carlo radiation transfer methods, which model the propagation of a polarised light sheet in the sample. Images of both reflecting and absorbing phantoms in a complex collagenous matrix were acquired, and the results for different polarisation configurations are compared. Focus scanning methods were then used to reduce noise and produce three-dimensional reconstructions of absorbing targets.

© 2016 Optical Society of America

Full Article  |  PDF Article
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References

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    [Crossref] [PubMed]

2016 (1)

2015 (3)

P. Llull, X. Yuan, L. Carin, and D. J. Brady, “Image translation for single-shot focal tomography,” Optica 2(9), 822–825 (2015).
[Crossref]

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

A. Bassi, B. Schmid, and J. Huisken, “Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development,” Development 142(5), 1016–1020 (2015).
[Crossref] [PubMed]

2014 (4)

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

S. Saghafi, K. Becker, C. Hahn, and H. U. Dodt, “3D-ultramicroscopy utilizing aspheric optics,” J. Biophotonics 7(1-2), 117–125 (2014).
[Crossref] [PubMed]

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2014).
[Crossref] [PubMed]

J. Mayer, A. Robert-Moreno, R. Danuser, J. V. Stein, J. Sharpe, and J. Swoger, “OPTiSPIM: integrating optical projection tomography in light sheet microscopy extends specimen characterization to nonfluorescent contrasts,” Opt. Lett. 39(4), 1053–1056 (2014).
[Crossref] [PubMed]

2013 (2)

2012 (2)

Y. Oshima, H. Sato, H. Kajiura-Kobayashi, T. Kimura, K. Naruse, and S. Nonaka, “Light sheet-excited spontaneous Raman imaging of a living fish by optical sectioning in a wide field Raman microscope,” Opt. Express 20(15), 16195–16204 (2012).
[Crossref]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

2011 (4)

B. A. Whitney, “Monte Carlo radiative transfer,” Bull. Astron. Soc. India 39, 101–127 (2011).

P. A. Santi, “Light sheet fluorescence microscopy: a review,” J. Histochem. Cytochem. 59(2), 129–138 (2011).
[Crossref] [PubMed]

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

G. Sena, Z. Frentz, K. D. Birnbaum, and S. Leibler, “Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy,” PLoS One 6(6), e21303 (2011).
[Crossref] [PubMed]

2008 (2)

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

E. Berrocal, E. Kristensson, M. Richter, M. Linne, and M. Aldén, “Application of structured illumination for multiple scattering suppression in planar laser imaging of dense sprays,” Opt. Express 16(22), 17870–17881 (2008).
[Crossref] [PubMed]

2007 (1)

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

2006 (1)

2005 (2)

2004 (2)

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

2002 (2)

S. L. Jacques, J. C. Ramella-Roman, and K. Lee, “Imaging skin pathology with polarized light,” J. Biomed. Opt. 7(3), 329–340 (2002).
[Crossref] [PubMed]

M. Shribak, S. Inoue, and R. Oldenbourg, “Polarization aberrations caused by differential transmission and phase shift in high-numerical-aperture lenses: theory, measurement, and rectification,” Opt. Eng. 41(5), 943–954 (2002).
[Crossref]

2000 (1)

S. L. Jacques, J. R. Roman, and K. Lee, “Imaging superficial tissues with polarized light,” Lasers Surg. Med. 26(2), 119–129 (2000).
[Crossref] [PubMed]

1999 (1)

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Aldén, M.

Amodaj, N.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

Anderson, C.

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Arganda-Carreras, I.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Backman, V.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Badizadegan, K.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Bassi, A.

A. Bassi, B. Schmid, and J. Huisken, “Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development,” Development 142(5), 1016–1020 (2015).
[Crossref] [PubMed]

Becker, K.

S. Saghafi, K. Becker, C. Hahn, and H. U. Dodt, “3D-ultramicroscopy utilizing aspheric optics,” J. Biophotonics 7(1-2), 117–125 (2014).
[Crossref] [PubMed]

Berent, J.

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

Berrocal, E.

Birnbaum, K. D.

G. Sena, Z. Frentz, K. D. Birnbaum, and S. Leibler, “Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy,” PLoS One 6(6), e21303 (2011).
[Crossref] [PubMed]

Brady, D. J.

Cardona, A.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Carin, L.

Chuai, M.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Danuser, R.

Dasari, R. R.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Dodt, H. U.

S. Saghafi, K. Becker, C. Hahn, and H. U. Dodt, “3D-ultramicroscopy utilizing aspheric optics,” J. Biophotonics 7(1-2), 117–125 (2014).
[Crossref] [PubMed]

Downie, H.

Dupuy, L. X.

Edelstein, A. D.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

Eliceiri, K.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Engelbrecht, C. J.

Federici, F.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Feld, M. S.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Forster, B.

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

Frentz, Z.

G. Sena, Z. Frentz, K. D. Birnbaum, and S. Leibler, “Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy,” PLoS One 6(6), e21303 (2011).
[Crossref] [PubMed]

Frise, E.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Glaser, A. K.

Gurjar, R.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Hahn, C.

S. Saghafi, K. Becker, C. Hahn, and H. U. Dodt, “3D-ultramicroscopy utilizing aspheric optics,” J. Biophotonics 7(1-2), 117–125 (2014).
[Crossref] [PubMed]

Hartenstein, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Haseloff, J.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Henricson, J.

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Huisken, J.

A. Bassi, B. Schmid, and J. Huisken, “Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development,” Development 142(5), 1016–1020 (2015).
[Crossref] [PubMed]

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2014).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Inoue, S.

M. Shribak, S. Inoue, and R. Oldenbourg, “Polarization aberrations caused by differential transmission and phase shift in high-numerical-aperture lenses: theory, measurement, and rectification,” Opt. Eng. 41(5), 943–954 (2002).
[Crossref]

Itzkan, I.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Jacques, S.

Jacques, S. L.

S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
[Crossref] [PubMed]

J. C. Ramella-Roman, S. A. Prahl, and S. L. Jacques, “Three Monte Carlo programs of polarized light transport into scattering media: part II,” Opt. Express 13(25), 10392–10405 (2005).
[Crossref] [PubMed]

S. L. Jacques, J. C. Ramella-Roman, and K. Lee, “Imaging skin pathology with polarized light,” J. Biomed. Opt. 7(3), 329–340 (2002).
[Crossref] [PubMed]

S. L. Jacques, J. R. Roman, and K. Lee, “Imaging superficial tissues with polarized light,” Lasers Surg. Med. 26(2), 119–129 (2000).
[Crossref] [PubMed]

Kajiura-Kobayashi, H.

Karjalainen, A. I.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Kaynig, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Keller, P. J.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

Kimura, T.

Knölker, H.-J.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Kristensson, E.

Leahy, M. J.

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Lee, K.

S. L. Jacques, J. C. Ramella-Roman, and K. Lee, “Imaging skin pathology with polarized light,” J. Biomed. Opt. 7(3), 329–340 (2002).
[Crossref] [PubMed]

S. L. Jacques, J. R. Roman, and K. Lee, “Imaging superficial tissues with polarized light,” Lasers Surg. Med. 26(2), 119–129 (2000).
[Crossref] [PubMed]

Leibler, S.

G. Sena, Z. Frentz, K. D. Birnbaum, and S. Leibler, “Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy,” PLoS One 6(6), e21303 (2011).
[Crossref] [PubMed]

Linne, M.

Liu, J. T. C.

Llull, P.

Longair, M.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

MacDonald, M. P.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Z. Yang, H. Downie, E. Rozbicki, L. X. Dupuy, and M. P. MacDonald, “Light Sheet Tomography (LST) for in situ imaging of plant roots,” Opt. Express 21(14), 16239–16247 (2013).
[Crossref] [PubMed]

Maizel, A.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Martin, R.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Mayer, J.

Naruse, K.

Nilsson, G. E.

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Nonaka, S.

O’Doherty, J.

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Oldenbourg, R.

M. Shribak, S. Inoue, and R. Oldenbourg, “Polarization aberrations caused by differential transmission and phase shift in high-numerical-aperture lenses: theory, measurement, and rectification,” Opt. Eng. 41(5), 943–954 (2002).
[Crossref]

Oshima, Y.

Perelman, L. T.

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

Peychl, J.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2014).
[Crossref] [PubMed]

Pietzsch, T.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Pinkard, H.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

Prahl, S.

Prahl, S. A.

Preibisch, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Ramella-Roman, J.

Ramella-Roman, J. C.

Reynaud, E. G.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2014).
[Crossref] [PubMed]

Richter, M.

Robert-Moreno, A.

Roman, J. R.

S. L. Jacques, J. R. Roman, and K. Lee, “Imaging superficial tissues with polarized light,” Lasers Surg. Med. 26(2), 119–129 (2000).
[Crossref] [PubMed]

Rozbicki, E.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Z. Yang, H. Downie, E. Rozbicki, L. X. Dupuy, and M. P. MacDonald, “Light Sheet Tomography (LST) for in situ imaging of plant roots,” Opt. Express 21(14), 16239–16247 (2013).
[Crossref] [PubMed]

Rueden, C.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Saalfeld, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Sage, D.

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

Saghafi, S.

S. Saghafi, K. Becker, C. Hahn, and H. U. Dodt, “3D-ultramicroscopy utilizing aspheric optics,” J. Biophotonics 7(1-2), 117–125 (2014).
[Crossref] [PubMed]

Sang, H. M.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Santi, P. A.

P. A. Santi, “Light sheet fluorescence microscopy: a review,” J. Histochem. Cytochem. 59(2), 129–138 (2011).
[Crossref] [PubMed]

Sato, H.

Schindelin, J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Schmid, B.

A. Bassi, B. Schmid, and J. Huisken, “Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development,” Development 142(5), 1016–1020 (2015).
[Crossref] [PubMed]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Schmidt, A. D.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

Sena, G.

G. Sena, Z. Frentz, K. D. Birnbaum, and S. Leibler, “Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy,” PLoS One 6(6), e21303 (2011).
[Crossref] [PubMed]

Sharpe, J.

Shribak, M.

M. Shribak, S. Inoue, and R. Oldenbourg, “Polarization aberrations caused by differential transmission and phase shift in high-numerical-aperture lenses: theory, measurement, and rectification,” Opt. Eng. 41(5), 943–954 (2002).
[Crossref]

Sjöberg, F.

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Song, F.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Stein, J. V.

Stelzer, E. H.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

C. J. Engelbrecht and E. H. Stelzer, “Resolution enhancement in a light-sheet-based microscope (SPIM),” Opt. Lett. 31(10), 1477–1479 (2006).
[Crossref] [PubMed]

Stelzer, E. H. K.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Stuurman, N.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

Swoger, J.

J. Mayer, A. Robert-Moreno, R. Danuser, J. V. Stein, J. Sharpe, and J. Swoger, “OPTiSPIM: integrating optical projection tomography in light sheet microscopy extends specimen characterization to nonfluorescent contrasts,” Opt. Lett. 39(4), 1053–1056 (2014).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Tinevez, J. Y.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Tomancak, P.

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2014).
[Crossref] [PubMed]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Tsuchida, M. A.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

Unser, M.

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

Vale, R. D.

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

Van De Ville, D.

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

von Wangenheim, D.

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

Wang, Y.

Weijer, C. J.

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

White, D. J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Whitney, B. A.

B. A. Whitney, “Monte Carlo radiative transfer,” Bull. Astron. Soc. India 39, 101–127 (2011).

Wittbrodt, J.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Yang, Z.

Yuan, X.

Biomed. Opt. Express (1)

Bull. Astron. Soc. India (1)

B. A. Whitney, “Monte Carlo radiative transfer,” Bull. Astron. Soc. India 39, 101–127 (2011).

Development (1)

A. Bassi, B. Schmid, and J. Huisken, “Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development,” Development 142(5), 1016–1020 (2015).
[Crossref] [PubMed]

IEEE J. Sel. Top. Quantum Electron. (1)

V. Backman, R. Gurjar, K. Badizadegan, I. Itzkan, R. R. Dasari, L. T. Perelman, and M. S. Feld, “Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ,” IEEE J. Sel. Top. Quantum Electron. 5(4), 1019–1026 (1999).
[Crossref]

J. Biol. Methods (1)

A. D. Edelstein, M. A. Tsuchida, N. Amodaj, H. Pinkard, R. D. Vale, and N. Stuurman, “Advanced methods of microscope control using μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref] [PubMed]

J. Biomed. Opt. (1)

S. L. Jacques, J. C. Ramella-Roman, and K. Lee, “Imaging skin pathology with polarized light,” J. Biomed. Opt. 7(3), 329–340 (2002).
[Crossref] [PubMed]

J. Biophotonics (1)

S. Saghafi, K. Becker, C. Hahn, and H. U. Dodt, “3D-ultramicroscopy utilizing aspheric optics,” J. Biophotonics 7(1-2), 117–125 (2014).
[Crossref] [PubMed]

J. Histochem. Cytochem. (1)

P. A. Santi, “Light sheet fluorescence microscopy: a review,” J. Histochem. Cytochem. 59(2), 129–138 (2011).
[Crossref] [PubMed]

Lasers Surg. Med. (1)

S. L. Jacques, J. R. Roman, and K. Lee, “Imaging superficial tissues with polarized light,” Lasers Surg. Med. 26(2), 119–129 (2000).
[Crossref] [PubMed]

Microsc. Res. Tech. (1)

B. Forster, D. Van De Ville, J. Berent, D. Sage, and M. Unser, “Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images,” Microsc. Res. Tech. 65(1-2), 33–42 (2004).
[Crossref] [PubMed]

Nat. Cell Biol. (1)

E. Rozbicki, M. Chuai, A. I. Karjalainen, F. Song, H. M. Sang, R. Martin, H.-J. Knölker, M. P. MacDonald, and C. J. Weijer, “Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation,” Nat. Cell Biol. 17(4), 397–408 (2015).
[Crossref] [PubMed]

Nat. Methods (2)

E. G. Reynaud, J. Peychl, J. Huisken, and P. Tomancak, “Guide to light-sheet microscopy for adventurous biologists,” Nat. Methods 12(1), 30–34 (2014).
[Crossref] [PubMed]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: An open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref] [PubMed]

Opt. Eng. (1)

M. Shribak, S. Inoue, and R. Oldenbourg, “Polarization aberrations caused by differential transmission and phase shift in high-numerical-aperture lenses: theory, measurement, and rectification,” Opt. Eng. 41(5), 943–954 (2002).
[Crossref]

Opt. Express (5)

Opt. Lett. (2)

Optica (1)

Phys. Med. Biol. (1)

S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
[Crossref] [PubMed]

Plant J. (1)

A. Maizel, D. von Wangenheim, F. Federici, J. Haseloff, and E. H. Stelzer, “High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy,” Plant J. 68(2), 377–385 (2011).
[Crossref] [PubMed]

PLoS One (1)

G. Sena, Z. Frentz, K. D. Birnbaum, and S. Leibler, “Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy,” PLoS One 6(6), e21303 (2011).
[Crossref] [PubMed]

Science (2)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. K. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

Skin Res. Technol. (1)

J. O’Doherty, J. Henricson, C. Anderson, M. J. Leahy, G. E. Nilsson, and F. Sjöberg, “Sub-epidermal imaging using polarized light spectroscopy for assessment of skin microcirculation,” Skin Res. Technol. 13(4), 472–484 (2007).
[Crossref] [PubMed]

Other (1)

C. F. Bohren and D. R. Huffman, Absorption and Scattering of Light by Small Particles (John Wiley & Sons, 2008).

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Figures (7)

Fig. 1
Fig. 1 Schematic of PLST setup (top view). ND-Neutral density filter, TE-Telescope, PF-Polarising filter, PL-Powell lens, CL-Cylindrical lens, Obj-Objective, PBS-Polarising Beam Splitter, TL-Tube lens.
Fig. 2
Fig. 2 Schematic describing the orientation of polarisation with respect to the light sheet. Linear polarisation in plane with the light sheet is described as perpendicular (s) polarised light, while light across the light sheet is described as parallel (p) polarised light.
Fig. 3
Fig. 3 Comparison of uniformity of (a) light sheet generated with just cylindrical lens and (b) light sheet generated using a combination of a Powell lens and cylindrical lens.
Fig. 4
Fig. 4 Normalised MCRT results, with overlay values representing signal to noise ratio (S/N) as a figure-of-merit, showing perpendicular-polarised illumination (central column, vertical arrow) and parallel-polarised illumination (right column, horizontal arrow). Figure parts (a) perpendicular illumination with non-analysed detection, (b) parallel illumination with non-analysed detection, (c) perpendicular illumination with co-polarised detection, (d) parallel illumination with cross-polarised detection, (e) perpendicular illumination with cross-polarised detection and (f) parallel illumination with co-polarised detection.
Fig. 5
Fig. 5 100 μm scattering spheres in a 10% w/v gelatine medium, imaged with perpendicular-polarised illumination (central column, vertical arrow) and parallel-polarised illumination (right column, horizontal arrow), with overlay values representing signal to noise as a figure-of-merit. Figure parts (a) perpendicular illumination with non-analysed detection, (b) parallel illumination with non-analysed detection, (c) perpendicular illumination with co-polarised detection, (d) parallel illumination with cross-polarised detection, (e) perpendicular illumination with cross-polarised detection and (f) parallel illumination with co-polarised detection.
Fig. 6
Fig. 6 Parallel illumination of the foam phantom with varying detection optics and colours. Each row represents a different detection of polarisation. Top row – unpolarised detection, (a) red channel, (b) green channel and (c) blue channel. Bottom row – co-polarised detection, (d) red channel, (e) green channel and (f) blue channel.
Fig. 7
Fig. 7 (a) Axial projection, (b) topology and (c) three-dimensional extended depth of field reconstruction of foam phantom using parallel co-polarised optics.

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